Search results for "Computation"
showing 10 items of 7362 documents
Evolutionary relationships among the members of an ancient class of non-LTR retrotransposons found in the nematode Caenorhabditis elegans.
1998
We took advantage of the massive amount of sequence information generated by the Caenorhabditis elegans genome project to perform a comprehensive analysis of a group of over 100 related sequences that has allowed us to describe two new C. elegans non-LTR retrotransposons. We named them Sam and Frodo. We also determined that several highly divergent subfamilies of both elements exist in C. elegans. It is likely that several master copies have been active at the same time in C. elegans, although only a few copies of both Sam and Frodo have characteristics that are compatible with them being active today. We discuss whether it is more appropriate under these circumstances to define only 2 elem…
Visualization in comparative music research
2007
Computational analysis of large musical corpora provides an approach that overcomes some of the limitations of manual analysis related to small sample sizes and subjectivity. The present paper aims to provide an overview of the computational approach to music research. It discusses the issues of music representation, musical feature extraction, digital music collections, and data mining techniques. Moreover, it provides examples of visualization of large musical collections.
G2(MP2) molecular orbital study of the substituent effect in the H3BPH3−nFn (n=0–3) donor–acceptor complexes
2000
Abstract The complexation energies of H3BPH3−nFn (n=0–3) and the proton affinities of PH3−nFn compounds have been investigated at the G2(MP2) level of theory. G2(MP2) results show that the successive fluorine substitution on the phosphine increases the stability of H3BPH3−nFn complexes although the basicity of the PH3−nFn ligands reduces with this substitution. The NBO partitioning scheme shows that this stability was related to the hyperconjugation effect. It proves also that the shortening of the P–H and P–F bond lengths, upon complexation, is due to an increasing `s' character in these bonds.
Experimental and theoretical study on the substitution reactions of aryl 2,4-dinitrophenyl carbonates with quinuclidines
2006
Abstract The reactions of quinuclidines with phenyl, 4-methylphenyl, and 4-chlorophenyl 2,4-dinitrophenyl carbonates are kinetically evaluated in aqueous solution. The Bronsted-type plots (log kN vs pKa of quinuclidinium ions) are linear. The magnitude of the slopes and validated theoretical scales of electrophilicity and nucleophilicity confirm the concerted nature of these reactions.
A comparative study of carboxy myoglobin in saccharide-water systems by molecular dynamics simulation.
2007
Results from room-temperature molecular dynamics simulation on a system containing carboxy-myoglobin, water, and maltose molecules are reported. Protein atomic fluctuations, protein−solvent and solvent−solvent hydrogen bonding have been analyzed and compared to the ones in trehalose−water and sucrose−water systems (Proteins 2005, 59, 291−302). Results help in rationalizing, at a molecular level, the effects of homologues disaccharides on protein structure/dynamics experimentally observed. Furthermore, the effectiveness of disaccharides in bioprotection in terms of peculiar protein−matrix coupling is also discussed.
3D MHD MODELING of TWISTED CORONAL LOOPS
2016
We perform MHD modeling of a single bright coronal loop to include the interaction with a non-uniform magnetic field. The field is stressed by random footpoint rotation in the central region and its energy is dissipated into heating by growing currents through anomalous magnetic diffusivity that switches on in the corona above a current density threshold. We model an entire single magnetic flux tube, in the solar atmosphere extending from the high-beta chromosphere to the low-beta corona through the steep transition region. The magnetic field expands from the chromosphere to the corona. The maximum resolution is ~30 km. We obtain an overall evolution typical of loop models and realistic loo…
Tracing the ICME plasma with a MHD simulation
2021
The determination of the chemical composition of interplanetary coronal mass ejection (ICME) plasma is an open issue. More specifically, it is not yet fully understood how remote sensing observations of the solar corona plasma during solar disturbances evolve into plasma properties measured in situ away from the Sun. The ambient conditions of the background interplanetary plasma are important for space weather because they influence the evolutions, arrival times, and geo-effectiveness of the disturbances. The Reverse In situ and MHD APproach (RIMAP) is a technique to reconstruct the heliosphere on the ecliptic plane (including the magnetic Parker spiral) directly from in situ measurements a…
A fast multi-dimensional magnetohydrodynamic formulation of the transition region adaptive conduction (TRAC) method
2021
We have demonstrated that the Transition Region Adaptive Conduction (TRAC) method permits fast and accurate numerical solutions of the field-aligned hydrodynamic equations, successfully removing the influence of numerical resolution on the coronal density response to impulsive heating. This is achieved by adjusting the parallel thermal conductivity, radiative loss, and heating rates to broaden the transition region (TR), below a global cutoff temperature, so that the steep gradients are spatially resolved even when using coarse numerical grids. Implementing the original 1D formulation of TRAC in multi-dimensional magnetohydrodynamic (MHD) models would require tracing a large number of magne…
Anhamonic finite temperature effects on the Raman and Infrared spectra to determine the crystal structure phase III of solid molecular hydrogen
2013
We present theoretical calculations of the Raman and IR spectra, as well as electronic properties at zero and finite temperature to elucidate the crystal structure of phase III of solid molecular hydrogen. We find that anharmonic finite temperature are particularly important and qualitatively influences the main conclusions. While P6$_3$/m is the most likely candidate for phase III at the nuclear ground state, at finite temperature the C2/c structure appears to be more suitable.
Lifetime of the superconductive state in short and long Josephson junctions
2008
We study the transient statistical properties of short and long Josephson junctions under the influence of thermal and correlated fluctuations. In particular, we investigate the lifetime of the superconductive metastable state finding the presence of noise induced phenomena. For short Josephson junctions we investigate the lifetime as a function both of the frequency of the current driving signal and the noise intensity and we find how these noise-induced effects are modified by the presence of a correlated noise source. For long Josephson junctions we integrate numerically the sine-Gordon equation calculating the lifetime as a function of the length of the junction both for inhomogeneous a…